The court is expected to decide the fate of the remaining sheep today.

Steve Meerwald, managing director of Australian export company Wellard, has seen footage of the slaughter and has described it as "gruesome".

"It made me ill and it still makes me appalled and disturbed just thinking about it," he said.

"It will be part of the process of determining who is responsible and accountable for this horrific act that has appalled people here in Pakistan just as much as it has appalled people outside of Pakistan."

As part of an overhaul of the industry last year, Senator Ludwig introduced a new system of regulation he called "supply chain assurance", which made the exporters responsible for how their animals are treated in the destination country.

He says the situation in Pakistan has been "unprecedented", but adds that anyone found guilty of breaching the new rules will be held to account.

Ms Parke says the Department of Agriculture has a conflict of interest and should not be responsible for investigating animal welfare complaints.

"Its job is to promote agriculture and primary produce, it's not the welfare of animals," she said.

The Department says no animals will be sent to Pakistan while it carries out a review into the latest incident.

In an announcement that made no reference to the live animal export issue, Prime Minister Julia Gillard said today that the head of the Agriculture Department, Conall O'Connell, had decided to stand down from the position early next year.

He'll be replaced by the head of the Immigration Department, Andrew Metcalfe, while Martin Bowles will take over from Mr Metcalfe.